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| Status |
Public on Dec 21, 2021 |
| Title |
Whole transcriptome analysis and functional studies reveal that senescence plays a pivotal role in Myotonic Dystrophy type 1 |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Myotonic dystrophy type 1 (DM1, MIM #160900) is an autosomal dominant disorder,
clinically characterized by progressive muscular weakness and multisystem degeneration.
The broad phenotypes observed in DM1 patients resemble the appearance of a multisystem accelerated aging process.
However, the molecular mechanisms underlying these phenotypes remain largely unknown.
Transcriptomic analysis of fibroblasts derived from DM1 patients and healthy individuals revealed a decrease in cell cycle activity,
cell division, and DNA damage response in DM1, all of which were required for the accumulation of cellular senescence.
Serial passage studies in vitro confirmed the accelerated increase in senescence and the acquisition of a senescence-associated secretory phenotype in DM1 fibroblasts.
Moreover, functional studies highlighted the impact of BMI-1/p16INK4a pathway dysregulation in DM1-associated cellular phenotypes.
Importantly, treatment with the senolytic compounds, quercetin, dasatinib, or navitoclax, reversed the accelerated aging phenotypes in both DM1 fibroblasts in vitro and in fruit flies in vivo.
Our results identified the accumulation of senescence-related processes as a major driver of DM1 pathophysiology and therefore,
demonstrated the efficacy of senolytic compounds in a pre-clinical setting.
This approach warrants further assessment as a novel therapeutic strategy for DM1.
Cell isolation and culture:
For the isolation of primary fibroblasts from healthy donors and DM1 patients (age range, 34 to 71),
punch skin biopsies were cut into 2–3 mm3 fragments and placed on a surface moistened with modified Eagle’s medium, containing 13% newborn calf serum,
0.4% penicillin/streptomycin (Gibco, Waltham, MA, USA) and 2 mM L-glutamine (Gibco).
Flasks were incubated vertically for 3–6 h at 37ºC under 5% CO2 and then returned to the horizontal position.
Human fibroblasts were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco) containing 10% fetal bovine serum (Sigma-Aldrich, St Louis, MO, USA),
1% L-glutamine (Gibco), and 1% penicillin–streptomycin (Gibco).
Fibroblasts were tested regularly for mycoplasma contamination.
Seven cultures from different DM1 patients and five from healthy controls were established.
Transcriptomic study and data analysis:
RNA was extracted from the fibroblasts from six DM1 patients and four age- and sex-matched controls at an early passage using TRIzol
(Life Technologies, Carlsbad, CA, USA).
Large-scale gene expression analysis was performed using the Human Clariom D microarray (Affymetrix, Santa Clara, CA, USA).
RNA integrity was confirmed using an RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).
Those samples with an RNA integrity value above 9 were used in the analysis.
A total of 300 ng of RNA from each sample was used for microarray analysis, following the manufacturer's instructions.
Microarray data analysis:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina).
Background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model.
Variance stabilization was performed using the log2 scaling,
and gene expression normalization was calculated with the method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in Matlab (MathWorks™).
The GO terms were taken from the AMIGO gene ontology database.
The significance of the GO terms of the DEGs was addressed calculating the P-values using an enrichment approach based on the hypergeometric distribution.
All the sets of GO terms were back-propagated from the final term appearing in the gene annotation to the root term of each GO.
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| Overall design |
10 samples were analyzed
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| Contributor(s) |
García-Puga1 M, Saenz-Antoñanzas A, Gerenu G, Arrieta A, Fernández-Torrón R, Zulaica M, Arauzo-Bravo M, Matheu A, de Munain AL |
| Citation(s) |
36040809 |
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| Submission date |
Dec 23, 2019 |
| Last update date |
Dec 08, 2022 |
| Contact name |
Marcos J. Araúzo-Bravo |
| E-mail(s) |
[email protected]
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| Phone |
+34 943 00 6108
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| Organization name |
Max Planck Institute for Molecular Biomedicine
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| Department |
Cell and Developmental Biology
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| Lab |
Computational Biology and Bionformatics
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| Street address |
Rogentstrasse
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| City |
Muenster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
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| Platforms (1) |
| GPL23126 |
[Clariom_D_Human] Affymetrix Human Clariom D Assay [transcript (gene) version] |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA597353 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE142542_RAW.tar |
235.5 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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